PCI partners with the Presbyterian Church in Brazil (IPB) and the Independent Presbyterian Church of Brazil (IPIB). The IPB was established by American Presbyterians in the 1860s, and it saw quick growth for a few decades. In 1902, the church divided and the IPIB was formed.

Today, the two churches enjoy good relations and both are involved in the training of ministers and Christian workers for outreach in most parts of Brazil. The IPIB trains lay missionaries in three centres; Cuiaba (West), Florianopolis (South) and Natal (Northeast).